There's a huge variety to excursions to choose from so it really depends on your interests. We were on the Sun Princess last May and I was very happy with the two we took:
In Juneau the 'Helicopter Glacier Discovery' - expensive, but worth every penny. The weather was bad most of that day and almost all flights were cancelled; but we were lucky, and on one of only two flights to go out of about twenty. There were only four passengers (normally six) and we got about ten min. extra 'air time' and spent twice as long on the glacier as normal.
In Skagway we took the 'Yukon Territory Adventure' bus tour. It leaves first thing in the morning and is rather long (about 7 hrs.) but has lots of stops. For about the same price as just going to the White Pass summit on the train, you continue on through Tormented Valley, the northwest tip of B.C. and to Frontier Heritage Village just beyond Carcross in the Yukon for a BBQed chicken lunch. We stopped at Carcross for about 1/2 hr. on the way back, and it had turned into a beautiful day for the ride back down to Skagway - spectacular! We asked to be dropped off 'downtown' and still had plenty of time to walk around Skagway when we got back.
In Ketchikan we did no tours, but I have read the Misty Fjords seaplane flightseeing is fantastic.
Last summer we cruised Alaska on the Vision of the Seas, and sent a daily report back to CruiseMates, along with pictures. Below is the link... the articles include excursions we did, and hopefully give a bit of a feeling of an Alaskan cruise.
Although there is so much in Alaska to see, my all time favorite shore excursion is flightseeing over Misty Fjord, an already glaciated part of southeast Alaska. You fly over fjords with waterfalls falling into them, mountain lakes (you even land in one). the silence is overwhelming. You, the other passengers, the crew and the plane are the only signs of human habitation on the earth. Absolutely awesome. I loved the helicopter tour, but the one that made the biggest difference for me was Misty Fjords.
Last June, we took the Dawn Princess to Alaska and the Inside Passage. In Juneau we did the Helicopter Glacier hike and Trek! We outfilled in climbing gear with the crampon's and ice pick and took a helicopter to Mendenhall Glacier. We received training in climbing ice flows (for those who need it.) My wife and me (with another couple) spend about 2 hours hiking up and down Mendenhall Glacier. Some of the climbing was vertical shears about 100 feet high!
It was great! What a rush! I want to go back and am planning to do the same trip, or maybe put together a hike/overnight to climb and scale the mountain behind Mendenhall Glacier, then overnight near the summit, then repel down with our gear on ropes.